GREMWI

Gradient-echo based (diffusion informed) myelin water imaging (GRE-MWI).

gpuGREMWI

Usage

obj = gpuGREMWI(te,fixed_params);
[out] = obj.estimate( data, mask, extraData, fitting);

Model parameters

% S0        : T1w signal [a.u.]
% MWF       : myelin water fraction [0,1]
% IWF       : intracellular volume ratio (=Vic or ICVF in DWI) [0,1]
% R2sMW     : R2* MW [1/s]
% R2sIW     : R2* IW [1/s]
% R2sEW     : R2* EW [1/s]
% freqMW    : frequency MW [ppm]
% freqIW    : frequency IW [ppm]
% dfreqBKG  : background frequency in addition to the one provided [ppm]
% dpini     : B1 phase offset in addition to the one provided [rad]
model_params    = { 'S0';   'MWF';  'IWF';  'R2sMW';'R2sIW';'R2sEW'; 'freqMW';'freqIW';'dfreqBKG';'dpini'};
ub              = [    2;     0.3;      1;      200;     50;     50;     0.25;    0.05;       0.4;   pi/2];
lb              = [    0;       0;      0;       50;      2;      2;    -0.05;    -0.1;      -0.4;  -pi/2];
startpoint      = [    1;     0.1;    0.8;      100;     15;     21;     0.04;       0;         0;      0];

I/O overview

obj = gpuMCRMWI(te,tr,fa,fixed_params);

Input	Description
te	1xNte echo time [s]
fixed_params	parameters to be fixed (Optional)
fixed_params.x_i	isotropic susceptibility of myelin [ppm], default = 0.1
fixed_params.x_a	anisotropic susceptibility of myelin [ppm], default = 0.1
fixed_params.E	exchange induced frequency shift [ppm], default = 0.02
fixed_params.rho_mw	myelin water proton ratio, default = 0.4186
fixed_params.B0	main magnetic field strength [T], default = 3
fixed_params.B0_dir	main magnetic field direction, [x,y,z], default = [0;0;1]

[out] = obj.estimate( data, mask, extraData, fitting);

Input	Description
data	5D MRI data, [x,y,z,t,fa]
mask	3D mask, [x,y,z]
extraData	Structure array with additional data
extraData.freqBKG	3D initial estimation of total field [Hz] (highly recommended), [x,y,z]
extraData.pini	3D initial estimation of B1 offset [rad] (highly recommended), [x,y,z]
extraData.ff	3D/4D fibre fraction map, [x,y,z,Nfibre] (for DIMWI only)
extraData.theta	3D/4D angle between B0 and fibre orientation, [x,y,z,Nfibre] (for DIMWI only)
extraData.fo	4D/5D fibre orientation vector map, [x,y,z,Nfibre,3] (for DIMWI only)
extraData.IWF	3D volume fraction Intracellular/(Intracellular+extracellular), [x,y,z] (for DIMWI only)
fitting	Structure array for model parameter estimation
fitting.optimiser	Algorithm for parameter update, ‘adam’ (default) | ‘sgdm’ | ‘rmsprop’
fitting.isdisplay	boolean, display optimisation process in graphic plot
fitting.convergenceValue	tolerance in loss gradient to stop the optimisation
fitting.convergenceWindow	# of elements in which ‘convergenceValue’ is computed
fitting.iteration	maximum # of optimisation iterations
fitting.initialLearnRate	initial learn rate of Adam optimiser
fitting.tol	tolerance in loss
fitting.lambda	regularisation parameter(s)
fitting.regmap	model parameter(s) in which regularisation is applied,
fitting.TVmode	Mode for total variation (TV) regularisation, ‘2D’ | ‘3D’
fitting.lossFunction	loss function, ‘L1’ | ‘L2’ | ‘huber’ | ‘mse’
fitting.isWeighted	is cost weighted, true|false, default = true
fitting.weightMethod	Weighting method, ‘1stecho’ (default) | ‘norm’
fitting.weightPower	power order of the weight, default = 2
fitting.DIMWI	Structure variable for DIMWI options
fitting.DIMWI.isFitIWF	‘IWF’ is a free parameter, default = true
fitting.DIMWI.isFitFreqMW	Myelin water frequency is a free parameter, default = true
fitting.DIMWI.isFitFreqIW	Intracellular water frequency is a free parameter, default = true
fitting.DIMWI.isFitR2sEW	Extracellular water R2* is a free parameter, default = true